Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrator

2013-01-19 Thread victor doss
gt; constraints, but here it's much more. >> I just found out that the SD update is not OpenMP threaded (and I even >> noted in the code why this is). >> I reopened the issue and will find a solution. >> >> Cheers. >> >> Berk >> >> --

RE: [gmx-users] >60% slowdown with GPU / verlet and sd integrator

2013-01-17 Thread Berk Hess
e non-bonded work, but that probably won't happen in 4.6. A solution might be buying a 3x a fast GPU. Cheers, Berk > Date: Thu, 17 Jan 2013 18:48:17 +0400 > Subject: Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrato

Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrator

2013-01-17 Thread James Starlight
>> noted in the code why this is). >> I reopened the issue and will find a solution. >> >> Cheers. >> >> Berk >> >> ---- >> > Date: Wed, 16 Jan 2013 16:20:32 +0100 >> > Subject: Re: [gmx-users] >60% slowdown with GPU /

Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrator

2013-01-16 Thread Szilárd Páll
lution. > > Cheers. > > Berk > > > > Date: Wed, 16 Jan 2013 16:20:32 +0100 > > Subject: Re: [gmx-users] >60% slowdown with GPU / verlet and sd > integrator > > From: mark.j.abra...@gmail.com > > To: gmx-users@gromacs.org > > > > We should proba

RE: [gmx-users] >60% slowdown with GPU / verlet and sd integrator

2013-01-16 Thread Berk Hess
ers. Berk > Date: Wed, 16 Jan 2013 16:20:32 +0100 > Subject: Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrator > From: mark.j.abra...@gmail.com > To: gmx-users@gromacs.org > > We should probably note this effect on the wiki somewhere? > > Mar

Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrator

2013-01-16 Thread Mark Abraham
----- > > Date: Wed, 16 Jan 2013 17:26:18 +0300 > > Subject: Re: [gmx-users] >60% slowdown with GPU / verlet and sd > integrator > > From: jmsstarli...@gmail.com > > To: gmx-users@gromacs.org > > > > Hi all! > > > > I've also done some calcu

RE: [gmx-users] >60% slowdown with GPU / verlet and sd integrator

2013-01-16 Thread Berk Hess
dmine issue: http://redmine.gromacs.org/issues/1121 Cheers, Berk > Date: Wed, 16 Jan 2013 17:26:18 +0300 > Subject: Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrator > From: jmsstarli...@gmail.com > To: gmx-users@gromacs.org

Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrator

2013-01-16 Thread James Starlight
Hi all! I've also done some calculations with the SD integraator used as the thermostat ( without t_coupl ) with the system of 65k atoms I obtained 10ns\day performance on gtc 670 and 4th core i5. I haventrun any simulations with MD integrator yet so It should test it. James 2013/1/15 Szilárd Pá

Re: [gmx-users] >60% slowdown with GPU / verlet and sd integrator

2013-01-15 Thread Szilárd Páll
Hi Floris, Great feedback, this needs to be looked into. Could you please file a bug report, preferably with a tpr (and/or all inputs) as well as log files. Thanks, -- Szilárd On Tue, Jan 15, 2013 at 3:50 AM, Floris Buelens wrote: > Hi, > > > I'm seeing MD simulation running a lot slower with